Abstract
During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.
Highlights
The breeding of rice (Oryza sativa L.) has produced new cultivars with favorable agronomic and economic characteristics such as biotic and abiotic stress resistance, high yield, and good eating quality
Structural changes of Japanese rice accessions following artificial selection To reveal the genetic relationships among the original landraces and the improved cultivars, we first classified the accessions into three groups based on the breeding phase: Group 1 (63 accessions) included landraces and cultivars bred before 1922; Group 2 (51 accessions) included cultivars bred from 1931 to 1974; and Group 3 (63 accessions) included cultivars bred from 1975 to 2005
The deviance information criterion (DIC) value decreased continuously as K increased from 2 to 10 and an optimal K value could not be estimated from the DIC values alone (Figure S2)
Summary
The breeding of rice (Oryza sativa L.) has produced new cultivars with favorable agronomic and economic characteristics such as biotic and abiotic stress resistance, high yield, and good eating quality. Identification of the genes involved in disease and insect resistance has enabled the incorporation of biotic stress resistance into elite cultivars, and the grain yield of modern cultivars improved at a rate of about 1% per year from 1966 to 1995 [2], such high gains in yield have not been achieved more recently. A rapid increase in yield from the 1950s to the 1970s in Japan was achieved by adopting modern high-yielding cultivars together with intensive culture [3]. After rice production for food was improved and Japan’s rice selfsufficiency approached 100%, the main breeding objective was changed from high yield to good eating quality [3]. The copious use of Koshihikari and related cultivars with good eating quality is evident in the pedigree of modern Japanese rice cultivars [4]
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